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One error problem occurred caused by data type during using GDCprepare function of TCGAbiolinks to handle TCGAbiolinks BRCA data
GDCRNATools
TCGA
4 weeks ago • updated 26 days ago
glaciya2018
• 0
0
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1
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270
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Error in GDCRNATools
ceRNA
GDCRNATools
RNASeq
updated 4 months ago by
Ram
▴ 210 • written 4 months ago by
Matvii Mykhailichenko
• 0
1
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1
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861
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How to sort out error in gdcCEAnalysis function of GDCRNATools R package?
GDCRNATools
updated 2.9 years ago by
James W. MacDonald
66k • written 2.9 years ago by
Bhavya
• 0
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Answer: LRT, pairwise comparisons and p-value adjustment
by
James W. MacDonald
66k
The convention is to adjust only within comparisons. But as the analyst, that's your call.
Comment: Counter-directional LFC shrinkage
by
ennui
• 0
Thank you for your response. The `ashr` shrinkage indeed preserves more of the original ranks in the data. So if I understand correctly, L…
Comment: Counter-directional LFC shrinkage
by
ennui
• 0
I agree it looks offset (and weird). The data is from NGS, not RNAseq, but we still want to see relative abundance between conditions - I t…
Comment: Running ENmix with mouse methylation manifest: readidat error - Error in readman
by
kred
• 0
I tried the latest version and encountered the same issues. The manifest file I downloaded is the .csv from the following link: https://em…
Comment: Error in gseDO function
by
Javier
• 0
As you say it is not a typical experiment of discovery, actually it is carried out in a different way, with a preselected set of genes. We …
Votes
Reduce the number of nodes appear in the cnetplot of clusterprofiler
A: DESeq2: add annotations (from data frame) to DESeqDataSet
Answer: Error in gseDO function
Comment: what the test method for enrichGO in clusterProfiler?
A: Comparison between two different group's pathway analysis results
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